SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples

  1. Javan Okendo
  2. Clarisse Musanabaganwa
  3. Peter Mwangi
  4. Martin Nyaga
  5. Harris Onywera

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Abstract

Proteome profile changes post-severe acute respiratory syndrome coronavirus 2 (post-SARS-CoV-2) infection in different body sites of humans remains an active scientific investigation whose solutions stand a chance of providing more information on what constitutes SARS-CoV-2 pathogenesis. While proteomics has been used to understand SARS-CoV-2 pathogenesis, there are limited data about the status of proteome profile in different human body sites infected by the SARS-CoV-2 virus. To bridge this gap, our study aims to characterize the proteins secreted in urine, bronchoalveolar lavage fluid (BALF), gargle solution, and nasopharyngeal samples and assess the proteome differences in these body samples collected from SARS-CoV-2-positive patients. We downloaded publicly available proteomic data from ( https://www.ebi.ac.uk/pride/ ). The data we downloaded had the following identifiers: (i) PXD019423, n = 3 from Charles Tanford Protein Center in Germany. (ii) IPX0002166000 , n = 15 from Beijing Proteome Research Centre, China. (iii) IPX0002429000 , n = 5 from Huazhong University of Science and Technology, China, and (iv) PXD022889, n = 18 from Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA. MaxQuant was used for the human peptide spectral matching using human and SARS-CoV-2 proteome database which we downloaded from the UniProt database (access date 13 th October 2021). The individuals infected with SARS-CoV-2 viruses displayed a different proteome diversity from the different body sites we investigated. Overally, we identified 1809 proteins across the four sample types we compared. Urine and BALF samples had significantly more abundant SARS-CoV-2 proteins than the other body sites we compared. Urine samples had 257(33.7%) unique proteins, followed by nasopharyngeal with 250(32.8%) unique proteins. Gargle solution and BALF had 38(5%) and 73(9.6%) unique proteins respectively. Urine, gargle solution, nasopharyngeal, and bronchoalveolar lavage fluid samples have different protein diversity in individuals infected with SARS-CoV-2. Moreover, our data also demonstrated that a given body site is characterized by a unique set of proteins in SARS-CoV-2 seropositive individuals.

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  1. Version published to 10.1371/journal.pone.0271870
  2. ScreenIT

    SciScore for 10.1101/2022.01.08.22268611: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    This study analyzed publicly available data downloaded from the Protein Identification Database, PRIDE (https://www.ebi.ac.uk/pride/) repository.
    PRIDE
    suggested: (Pride-asap, RRID:SCR_012052)
    https://www.ebi.ac.uk/pride/
    suggested: (Proteomics Identifications (PRIDE, RRID:SCR_003411)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    This study had some limitations. The first limitation is the small sample size, but this did not affect our understanding of the biology under study. We also acknowledge the difference in the sample preparation protocols, which could also be a potential confounder. This is secondary data analysis; we did not have sufficient study participants’ information, and we acknowledge this because it can contribute to the inaccurate interpretation of the results.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2022.01.08.22268611v1 on medRxiv
  4. Version published to 10.1101/2022.01.08.22268611v2 on medRxiv